Say I have three names viz... Firstname Middlename Surname. My first name is quite long. My supervisor is requesting that I only use my Middle and Surnames. This occured with my first manuscript with him (he has two short names). Although, I have one publication (with my full three names) before studying under my current supervisor, I have tried to do this. My ORCID account contains the three names. IEEE membership name emphasizes my Firstname and Surname. My question is if I would like to use only my Middle and Surnames now, what are the things I must do and precautions to take to ensure consistency and avoid complications in the future.
Use the name that you wish to be known by within academia. For the next 40 years (depending on age and career), you will build a reputation attached to your name. That name will be on your papers, announcing you for presentations, on your name tag at conferences, as the author of any books you publish and for many other uses.
Your supervisor is not asking for a trivial change for his or her convenience, your supervisor is asking for you to either give up your preferred name throughout your career, or to have multiple names on publications. While it is certainly fixable to have multiple names, it is harder to ensure you get credit for all your work.
You could perhaps ask why your supervisor wants you to use a different name. There may be a good reason in which case you can take that into account in your decision. Since you have a long name, do people use the full name when addressing you? Would it be reasonable to use perhaps a shorter version of your first name if that's how you are known?